| 02709d2 | apregier | 12 December 2012, 18:52:58 UTC | Merge branch 'fix' into gb_master | 12 December 2012, 18:52:58 UTC |
| f68a276 | apregier | 12 December 2012, 18:52:40 UTC | Update expected test output | 12 December 2012, 18:52:47 UTC |
| 5929d90 | Nathan Nutter | 12 December 2012, 18:11:13 UTC | Revert "refactor conditionals as hash" This reverts commit d7cd9e067a071ecc737fd90a6dad783d1727c809. | 12 December 2012, 18:11:28 UTC |
| 0f8f1fa | apregier | 12 December 2012, 18:10:09 UTC | Merge branch 'fix' into gb_master | 12 December 2012, 18:10:09 UTC |
| 1272f1e | apregier | 12 December 2012, 18:09:29 UTC | Improve RAM reservation calculation for allpaths | 12 December 2012, 18:09:29 UTC |
| 812256c | Nathan Nutter | 11 December 2012, 19:10:48 UTC | add genome-prove commands CHANGELOG: You can now use `genome-prove` to launch a REPL instead of using `prove` which may not use the correct Perl version depending on your environment. | 11 December 2012, 19:10:48 UTC |
| 9acc78f | Nathan Nutter | 11 December 2012, 18:57:38 UTC | add genome-re.pl commands CHANGELOG: You can now use `genome-re.pl` to launch a REPL instead of using `re.pl` which may not use the correct Perl version depending on your environment. | 11 December 2012, 19:09:33 UTC |
| d7cd9e0 | Nathan Nutter | 11 December 2012, 00:02:43 UTC | refactor conditionals as hash | 11 December 2012, 19:09:33 UTC |
| 7e72601 | APipe Tester | 11 December 2012, 18:11:45 UTC | updated graphite submodule to 495c2b8 | 11 December 2012, 18:11:45 UTC |
| e4f3c1a | Gabriel Sanderson | 10 December 2012, 23:02:28 UTC | Merge branch 'master' into gb_master | 10 December 2012, 23:02:28 UTC |
| f3a20ce | Gabriel Sanderson | 10 December 2012, 23:02:04 UTC | _check_instance_output: Change the if statement such that it will automatically clean up symlinks that point to nowhere (as intended). | 10 December 2012, 23:02:04 UTC |
| 078561e | apregier | 10 December 2012, 22:17:57 UTC | Merge branch 'fix' into gb_master | 10 December 2012, 22:17:57 UTC |
| 5e453f8 | apregier | 10 December 2012, 22:17:23 UTC | Improve estimation of build directory size for allpaths | 10 December 2012, 22:17:37 UTC |
| 3059717 | Anthony Brummett | 10 December 2012, 22:14:31 UTC | Allow it to run in cases where 0 reads are in the output metrics count | 10 December 2012, 22:14:31 UTC |
| 3f954b0 | Thomas Mooney | 10 December 2012, 21:11:17 UTC | Use some "reads" generated based on a known gene so Tophat finds alignments. | 10 December 2012, 21:11:17 UTC |
| 56107c1 | APipe Tester | 10 December 2012, 20:09:42 UTC | Merge remote-tracking branch 'origin/master' | 10 December 2012, 20:09:42 UTC |
| 19eff5e | Scott Smith | 10 December 2012, 19:55:01 UTC | added GENOME_SYS_GROUP to control default Unix group for created files/directories | 10 December 2012, 19:55:01 UTC |
| 7400590 | Malachi Griffith | 10 December 2012, 19:51:27 UTC | Up max allowed snvs/indels for mutation-diagram generation in clin-seq | 10 December 2012, 19:51:27 UTC |
| 1276d8d | Nathan Nutter | 10 December 2012, 19:41:31 UTC | second attempt at fix for creating temp dir on use - forgot to run tests on previous attempt - the tests needs the values in order to create a command string | 10 December 2012, 19:42:42 UTC |
| 31744c8 | Thomas Mooney | 10 December 2012, 18:51:53 UTC | Preserve the desired bowtie-version so we get the right path variable. | 10 December 2012, 18:51:53 UTC |
| 9964a93 | Nathan Nutter | 10 December 2012, 17:39:05 UTC | tests should not exit | 10 December 2012, 17:40:25 UTC |
| ef7786c | Nathan Nutter | 10 December 2012, 17:38:45 UTC | fix for creating temp dir on use | 10 December 2012, 17:40:24 UTC |
| 6ac984d | Nathan Nutter | 10 December 2012, 17:03:08 UTC | Merge "Add command to blacklist segments" | 10 December 2012, 17:03:08 UTC |
| d107953 | Thomas Mooney | 10 December 2012, 15:21:33 UTC | Ignore the index file when diffing--just lists other files. | 10 December 2012, 15:21:33 UTC |
| 262e38f | dmorton | 06 December 2012, 03:51:44 UTC | Add command to blacklist segments Change-Id: Ib42cb26791722c5b260f4dcf141975334a9b0cd0 | 10 December 2012, 15:07:37 UTC |
| 4378919 | Scott Smith | 10 December 2012, 04:54:40 UTC | remove check that a model id is an integer so that the code will work with UUID model IDs | 10 December 2012, 04:54:40 UTC |
| 0b51bb2 | Malachi Griffith | 10 December 2012, 00:34:26 UTC | Minor bug fix in clinseq-update analysis | 10 December 2012, 00:34:26 UTC |
| 95feb3e | Scott Smith | 09 December 2012, 08:50:09 UTC | updated weka InlineConfig64 | 09 December 2012, 08:50:09 UTC |
| cea5838 | Scott Smith | 09 December 2012, 08:47:27 UTC | eliminate all warnings during compile of Genome/ modules | 09 December 2012, 08:47:27 UTC |
| b8bde9b | Scott Smith | 09 December 2012, 08:23:11 UTC | made target_region_set_name optional on refalign ...somehow this dodges a check | 09 December 2012, 08:23:11 UTC |
| e11042c | Scott Smith | 09 December 2012, 08:06:43 UTC | ensure fasta chunker does not create directories at compile time | 09 December 2012, 08:06:43 UTC |
| b2b9916 | Scott Smith | 09 December 2012, 08:05:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 December 2012, 08:05:15 UTC |
| 5a19cd4 | Scott Smith | 09 December 2012, 08:04:33 UTC | updated clinseq docs so that Define-docs.t passes | 09 December 2012, 08:04:33 UTC |
| 3b33258 | Malachi Griffith | 09 December 2012, 00:56:08 UTC | Added tool to create simplified VCF from somatic-variation build dir that contains only one column per sample and only hq passing somatic variants | 09 December 2012, 00:56:08 UTC |
| f995271 | Malachi Griffith | 09 December 2012, 00:19:38 UTC | Bug fixes to clin-seq edge cases in dump-igv-xml (undefined sample common name) and cn-view (no cnvhmm segments) | 09 December 2012, 00:19:38 UTC |
| 0beb369 | Scott Smith | 08 December 2012, 23:33:58 UTC | Update how clinseq calls SummarizeTier1SnvSupport. The previous commit failed to pass along all builds, and failed to set a true return value on success. | 08 December 2012, 23:33:58 UTC |
| fb84098 | Scott Smith | 08 December 2012, 21:34:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 08 December 2012, 21:34:07 UTC |
| 08ea277 | Scott Smith | 08 December 2012, 21:33:58 UTC | moved md5sum methods from internal to published portion of Genome::Sys | 08 December 2012, 21:33:58 UTC |
| da29fea | APipe Tester | 08 December 2012, 21:31:56 UTC | updated ur submodule to 27e73cf | 08 December 2012, 21:31:56 UTC |
| ecc8753 | Scott Smith | 08 December 2012, 20:18:54 UTC | fixed error pulling position files | 08 December 2012, 20:18:54 UTC |
| 4e83325 | Scott Smith | 07 December 2012, 23:24:20 UTC | fixed typo in package name for clinseq SummarizeTier1SnvSupport | 07 December 2012, 23:24:20 UTC |
| 30717b9 | Scott Smith | 07 December 2012, 20:17:12 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 07 December 2012, 20:17:12 UTC |
| 5af9868 | Scott Smith | 07 December 2012, 20:17:00 UTC | added clinseq step SummarizeTier1SnvSupport.pm and SummarizeTier1SnvSupport.pm.R | 07 December 2012, 20:17:00 UTC |
| 9b337fe | Nathan Nutter | 07 December 2012, 19:43:04 UTC | add comment about RT #88011 | 07 December 2012, 19:43:04 UTC |
| b1ac3ac | Nathan Nutter | 07 December 2012, 19:41:40 UTC | re-enable | 07 December 2012, 19:41:56 UTC |
| 586ae40 | Malachi Griffith | 07 December 2012, 17:50:15 UTC | Update test results in clin-seq to account for update to update-analysis | 07 December 2012, 17:50:15 UTC |
| 47a767c | Malachi Griffith | 07 December 2012, 16:39:06 UTC | Update clin-seqs definition of a tumor sample to include PIN lesions | 07 December 2012, 16:39:06 UTC |
| c2e65b3 | Malachi Griffith | 07 December 2012, 16:28:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Model/ClinSeq/Command/Main.pm | 07 December 2012, 16:28:48 UTC |
| 33372e9 | Malachi Griffith | 07 December 2012, 16:25:47 UTC | Update to clin-seq main class to handle cases without WGS data | 07 December 2012, 16:25:47 UTC |
| d203490 | Travis Abbott | 07 December 2012, 05:46:08 UTC | add test version of ibwa 0.5 | 07 December 2012, 05:46:08 UTC |
| 949092c | Scott Smith | 07 December 2012, 00:06:05 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 07 December 2012, 00:06:05 UTC |
| a0fbda1 | Scott Smith | 07 December 2012, 00:05:55 UTC | the BAM readcounts for tier 1 SNVs are now done in parallel | 07 December 2012, 00:05:55 UTC |
| 2871cec | APipe Tester | 07 December 2012, 00:05:11 UTC | updated ur submodule to ae12ee1 | 07 December 2012, 00:05:11 UTC |
| 4a0d829 | Thomas Mooney | 06 December 2012, 23:43:34 UTC | Handle contig names with "|" or similar characters by not interpolating input. | 06 December 2012, 23:43:34 UTC |
| 41d34ad | Travis Abbott | 06 December 2012, 22:57:52 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 December 2012, 22:57:52 UTC |
| 56fc35a | Travis Abbott | 06 December 2012, 22:57:11 UTC | use sample names instead of ids in vcf header in gmt vcf create-cross-sample-vcf (indels) | 06 December 2012, 22:57:11 UTC |
| b58fcf7 | Eddie Belter | 06 December 2012, 22:17:01 UTC | Sync: Add sample attr class | 06 December 2012, 22:17:01 UTC |
| bb9e8cb | Thomas Mooney | 06 December 2012, 21:49:38 UTC | First draft of stapling SV assembly validation to end of pipeline. TODO: Bring the pieces up to standards instead of stapling what we've got. | 06 December 2012, 21:49:38 UTC |
| 3447420 | Obi Griffith | 06 December 2012, 21:35:34 UTC | updated archive commands to reflect new tutorial | 06 December 2012, 21:35:34 UTC |
| 80dcdc2 | apregier | 06 December 2012, 21:09:30 UTC | Merge branch 'vep' into gb_master | 06 December 2012, 21:09:30 UTC |
| 5f5fde3 | apregier | 06 December 2012, 15:23:44 UTC | Add Rsid column to the annotation file in somatic variation | 06 December 2012, 20:24:42 UTC |
| 9bfc4db | Travis Abbott | 06 December 2012, 19:50:22 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 December 2012, 19:50:22 UTC |
| 12ec882 | Travis Abbott | 06 December 2012, 19:49:59 UTC | bump vcf version for samtools indel -> vcf fixes | 06 December 2012, 19:49:59 UTC |
| 89a77f1 | Nathan Nutter | 06 December 2012, 19:48:56 UTC | fix incorrect output_files | 06 December 2012, 19:49:03 UTC |
| 55948bd | Travis Abbott | 06 December 2012, 19:46:50 UTC | fix samtools indel -> vcf converter it wasn't handling multiple deletions or calls with an insertion and a deletion properly. | 06 December 2012, 19:46:50 UTC |
| b0e5832 | Nathan Nutter | 06 December 2012, 19:32:39 UTC | whitespace | 06 December 2012, 19:35:05 UTC |
| 4bf70f5 | Nathan Nutter | 06 December 2012, 19:32:27 UTC | fix missing package | 06 December 2012, 19:35:05 UTC |
| 9357359 | Nathan Nutter | 06 December 2012, 19:32:05 UTC | fix missing package | 06 December 2012, 19:35:05 UTC |
| fabf259 | APipe Tester | 06 December 2012, 19:24:32 UTC | updated ur submodule to 1037f9d | 06 December 2012, 19:24:32 UTC |
| b902b1d | Nathan Nutter | 06 December 2012, 19:05:44 UTC | fix typo, early paren | 06 December 2012, 19:05:44 UTC |
| 700841e | Nathan Nutter | 06 December 2012, 19:05:29 UTC | whitespace | 06 December 2012, 19:05:29 UTC |
| 1c54cde | APipe Tester | 06 December 2012, 16:39:10 UTC | Merge remote-tracking branch 'origin/master' | 06 December 2012, 16:39:10 UTC |
| c3b452a | Thomas Mooney | 06 December 2012, 15:50:00 UTC | Report errors mapping workflow inputs. | 06 December 2012, 15:50:00 UTC |
| 2225614 | Nathan Nutter | 06 December 2012, 15:13:17 UTC | Merge "fix bug with unarchiving and moving disk allocaitons" | 06 December 2012, 15:13:17 UTC |
| 2e41682 | Nathan Nutter | 06 December 2012, 03:18:47 UTC | disable | 06 December 2012, 03:18:47 UTC |
| 6fb0472 | Nathan Nutter | 06 December 2012, 01:44:31 UTC | fix for running with UR_DBI_NO_COMMIT - disable UR_DBI_NO_COMMIT for the ur command - grep out undefined rows, etc. | 06 December 2012, 01:44:31 UTC |
| e845110 | Nathan Nutter | 06 December 2012, 00:44:16 UTC | add a couple additional tests - make sure we are in Genome, test failure implied that maybe we aren't - check that ur command exits 0 | 06 December 2012, 00:45:38 UTC |
| 73f8cd1 | Nathan Nutter | 05 December 2012, 23:25:51 UTC | child_exit_code is system exit_cide >> 8 | 05 December 2012, 23:53:43 UTC |
| 2de7575 | Nathan Nutter | 05 December 2012, 21:21:07 UTC | add test to prevent ambiguous property definitions on SoftwareResult subclasses | 05 December 2012, 23:53:42 UTC |
| 5692d36 | Nathan Nutter | 05 December 2012, 21:20:39 UTC | flag more SoftwareResult subclass ambiguous properties | 05 December 2012, 23:53:42 UTC |
| 79c49ab | Scott Smith | 05 December 2012, 21:31:43 UTC | updated to connect the Main result to the output connector for cases in which no steps follow main b/c there is no WGS data. | 05 December 2012, 21:31:43 UTC |
| 981fdc2 | Malachi Griffith | 05 December 2012, 21:15:22 UTC | Various minor updates to druggable-gene importer code | 05 December 2012, 21:15:22 UTC |
| 3db84e6 | Charles Lu | 05 December 2012, 21:08:50 UTC | added documentation | 05 December 2012, 21:08:50 UTC |
| daca5be | Charles Lu | 05 December 2012, 20:53:08 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 December 2012, 20:53:08 UTC |
| 222d195 | Charles Lu | 05 December 2012, 20:53:01 UTC | addeds extra column with GMAF information | 05 December 2012, 20:53:01 UTC |
| 02c4dcd | Kyung Kim | 05 December 2012, 20:33:38 UTC | Updated to make contigs.cmt file in velvet pipeline | 05 December 2012, 20:33:38 UTC |
| deb36bc | Kyung Kim | 05 December 2012, 19:58:59 UTC | Update for new velvet cmt-file tool | 05 December 2012, 19:58:59 UTC |
| 57fcec0 | Kyung Kim | 05 December 2012, 19:58:29 UTC | New velvet tool to create assembly cmt file | 05 December 2012, 19:58:29 UTC |
| 9db39b7 | APipe Tester | 05 December 2012, 19:19:51 UTC | updated jenkins submodule to 9fac041 | 05 December 2012, 19:19:51 UTC |
| 05efa73 | dmorton | 05 December 2012, 18:21:37 UTC | Make 'genome software-result set-test-name' easier to use | 05 December 2012, 18:22:53 UTC |
| 0729939 | APipe Tester | 05 December 2012, 18:11:25 UTC | updated ur submodule to e31ea0e | 05 December 2012, 18:11:25 UTC |
| 87650be | Malachi Griffith | 05 December 2012, 17:25:16 UTC | Added a new druggable-gene importer for TEND: trends in the exploitation of drug targets | 05 December 2012, 17:25:16 UTC |
| 6450f68 | Malachi Griffith | 05 December 2012, 17:24:16 UTC | Update base sub-routines for downloading source in druggable-gene | 05 December 2012, 17:24:16 UTC |
| 804ab90 | Mark Burnett | 05 December 2012, 16:47:22 UTC | fix bug with unarchiving and moving disk allocaitons There were cases where a shadow allocation might not be deleted if an error occurred. This caused subsequent attempts to move or unarchive the same allocation to fail as well. Change-Id: I6e8c20b42d99f05332515b7fb7ac0a5177ee7f99 | 05 December 2012, 16:48:52 UTC |
| 78a0eba | Mark Burnett | 05 December 2012, 15:38:34 UTC | add field Disk::Volume to fix the issues caused by RT #88076 | 05 December 2012, 15:38:34 UTC |
| b6c7e53 | Mark Burnett | 05 December 2012, 15:14:10 UTC | remove SR:Command:FixLookupHashesDV2 We decided to just give the broken results a new test_name. | 05 December 2012, 15:15:58 UTC |
| ade64a3 | Mark Burnett | 05 December 2012, 15:13:22 UTC | make filter_version optional in DV2:R:Vcf:Filter | 05 December 2012, 15:15:58 UTC |
| 821797a | Thomas Mooney | 05 December 2012, 15:07:31 UTC | Also update the list of command names (so tab-completion finds them). | 05 December 2012, 15:07:31 UTC |
| 8ff3626 | Adam Coffman | 04 December 2012, 22:31:24 UTC | Deep copy isn't needed here, and in fact breaks UR's object cache. When the copy goes out of scope, it fires the destroy handler and the original object is cleared too. | 04 December 2012, 22:31:24 UTC |
| 5b237c3 | Gabriel Sanderson | 04 December 2012, 21:54:44 UTC | Merge branch 'master' into gb_master | 04 December 2012, 21:54:44 UTC |
